JCS Cache now uses Long objects for keys
The serialization of Alignment objects does not involved serializing the
SAMHeader object (reducing the size of the object serialized).
StrandedCountScore & StrandedScanStatisticScore are added
Added CalculateUsableReadsStatistics class
Synchronized with the last commit by Mitch. Most differences in the
classes are due to spacing differences on each line.
Merge branch 'master' of https://github.com/mgarber/scriptureV2.git

Conflicts:
	.classpath
	src/java/nextgen/core/scripture/BuildScriptureCoordinateSpace.java
	src/java/nextgen/core/writers/PairedEndWriter.java